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...useful to some. -------- Original Message -------- Subject: Mac OS X builds of CelQuantileNorm, vcftools/samtools/tabix, and snpStats Date: Wed, 14 Mar 2012 02:59:42 +0000 (GMT) From: Hin-Tak Leung <htl10 at users.sourceforge.net> Reply-To: htl10 at users.sourceforge.net To: bonsai list <outmodedbonsai-announce at lists.sourceforge.net> CelQantileNorm, vcftools/samtools/tabix are bult for Mac OS X. These are universal binaries and work for all recent variants of Powerpc-, Intel 32-bit/64-bit Macs. snpStats 1.5.5 (out a week ago) turned out to be "differently buggy" from previous...

...soft windows' system fonts. So there is a 2.5.2. There are new 2.5.2 bundles for windows & Mac OS X. The official win/mac binaries of R were built statically with 2+-years-old freetype with a few known problems. Most should upgrade/rebuild. >> >> http://sourceforge.net/projects/outmodedbonsai/files/R/ >> >> - problem with the survival package: >> >> Trying to re-run a vignette to get the same result as two years ago >> reveal a strange change. I went and bisected it down to >> r11513 and r11516 of the survival package. >> >> -----------...

I have had some fun in the last few days trying to put together an annotated map of China with R and some public GIS data: http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/1.17.7.11/China_Choropleth_Maps.pdf/download It is done, and rather nice... there are a few issues: - the default pdf() device cannot do CJK with embedded fonts - and cairo_pdf() is not hooked up to Sweave yet. I have had a quick look, and it does not look too complicated,...

The windows replacement is R-library-grDevices-libs-winCairo_20150122.zip in http://sourceforge.net/projects/outmodedbonsai/files/R/ The cairo replacements are just two bundles, windows or OS X - containing replacements for R 2.15.3, 3.0.3 and 3.1.2. You just extract the relevant one for your R version. The windows builds of R packages snpStats x.x.x.8 and snpMatrix 1.19.0.20 were done with link-time optimization. (up...

Just before the holiday, I asked the freetype developers what is the context of these two comments about freetype in the code of R's grDevices: ======= R/src/library/grDevices/src/cairo/cairoFns.c around line 720 ===== /* some FreeType versions have broken index support, fall back to index 0 */ if (!FT_New_Face(ft_library, (const char *) file, index, &face) || (index

Just before the holiday, I asked the freetype developers what is the context of these two comments about freetype in the code of R's grDevices: ======= R/src/library/grDevices/src/cairo/cairoFns.c around line 720 ===== /* some FreeType versions have broken index support, fall back to index 0 */ if (!FT_New_Face(ft_library, (const char *) file, index, &face) || (index

...Mon, 2/20/17, Martin Maechler <maechler at stat.math.ethz.ch> wrote: Subject: Re: [Rd] another fix for R crashes under enable-strict-barrier, lto, trunk at 72156 To: "Hin-Tak Leung" <htl10 at users.sourceforge.net> Cc: r-devel at r-project.org, "bonsai list" <outmodedbonsai-announce at lists.sourceforge.net> Date: Monday, February 20, 2017, 9:56 AM >>>>> Hin-Tak Leung <htl10 at users.sourceforge.net> >>>>>? ???on Sat, 11 Feb 2017 19:30:26 +0000 writes: ? ? > I haven' t touched R for some 18 months, and so I have n...

...port: (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14645) Illumina's cluster definition files (*.egt) are one of the proprietary and undocumented file formats used by their GenomeStudio line of products for genomic studies. snpMatrix 1.17.0.7 onwards (http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/) contains codes for reading that file format, as well as two example files of such type generated from public data, and also a vignette demonstrating their usefulness and relevance to genomic studies. R svn check (the upcoming 2.14) mis-identifies those bundled files as und...

...nough to go into trunk and 2.14.1? --- On Sat, 22/10/11, Hin-Tak Leung <htl10 at users.sourceforge.net> wrote: > I have had some fun in the last few > days trying to put together an annotated map of China with R > and some public GIS data: > > http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/1.17.7.11/China_Choropleth_Maps.pdf/download > > It is done, and rather nice... there are a few issues: > > - the default pdf() device cannot do CJK with embedded > fonts - and cairo_pdf() is not hooked up to Sweave yet. I > have had a quick look, and it d...

R.framework-Versions-Resources-library-grDevices-libs-cairo_20150120.tgz in http://sourceforge.net/projects/outmodedbonsai/files/R/ are dropped in replacement to the cairo.so's in the official R binaries (2.15.3, 3.0.3, 3.1.2). updated to cairo-1.12.18 and freetype-2.5.4. The official R binaries' were built with early freetype 2.4.x and cairo 1.11(?) and had a number of issues with some windows and mac system...